Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data.

Understanding the genetic characteristics of indigenous goat breeds is crucial for their conservation and breeding efforts. Hainan black goats, as a native breed of south China's tropical island province of Hainan, possess distinctive traits such as black hair, a moderate growth rate, good meat quality, and small body size. However, they exhibit exceptional resilience to rough feeding conditions, possess high-quality meat, and show remarkable resistance to stress and heat. In this study, we resequenced the whole genome of Hainan black goats to study the economic traits and genetic basis of these goats, we leveraged whole-genome sequencing data from 33 Hainan black goats to analyze single nucleotide polymorphism (SNP) density, Runs of homozygosity (ROH), Integrated Haplotype Score (iHS), effective population size (Ne), Nucleotide diversity Analysis (Pi) and selection characteristics. Our findings revealed that Hainan black goats harbor a substantial degree of genetic variation, with a total of 23 608 983 SNPs identified. Analysis of ROHs identified 53 710 segments, predominantly composed of short fragments, with inbreeding events mainly occurring in ancient ancestors, the estimates of inbreeding based on ROH in Hainan black goats typically exhibit moderate values ranging from 0.107 to 0.186. This is primarily attributed to significant declines in the effective population size over recent generations. Moreover, we identified 921 candidate genes within the intersection candidate region of ROH and iHS. Several of these genes are associated with crucial traits such as immunity (PTPRC, HYAL1, HYAL2, HYAL3, CENPE and PKN1), heat tolerance (GNG2, MAPK8, CAPN2, SLC1A1 and LEPR), meat quality (ACOX1, SSTR1, CAMK2B, PPP2CA and PGM1), cashmere production (AKT4, CHRM2, OXTR, AKT3, HMCN1 and CDK19), and stress resistance (TLR2, IFI44, ENPP1, STK3 and NFATC1). The presence of these genes may be attributed to the genetic adaptation of Hainan black goats to local climate conditions. The insights gained from this study provide valuable references and a solid foundation for the preservation, breeding, and utilization of Hainan black goats and their valuable genetic resources.

Genome-wide scans for selection signatures in indigenous chickens reveal candidate genes associated with local adaptation.

Population growth and climate change pose challenges to the sustainability of poultry farming. The emphasis on high-yield traits in commercialized breeds has led to a decline in their adaptability. Chicken varieties adapted to the local environment, possessing traits that facilitate adaptation to climate change, such as disease resistance and tolerance to extreme weather conditions, can improve hybridization outcomes. In this study, we conducted an analysis of the population structure and genetic diversity of 110 chickens representing indigenous breeds from southern China and two different commercial breeds. Further, we performed comparative population genomics, utilizing nucleotide diversity and fixation statistics, to characterize genomic features of natural selection and to identify unique genetic traits and potential selection markers developed by indigenous breeds after adapting to the local environment. Results based on genetic diversity and population structure analyses showed that indigenous varieties exhibited high levels of genetic diversity. Commercial breeds that have been indigenously bred demonstrated higher levels of genetic diversity than those that have not, and breeds with different selection practices displayed significant differences in genetic structure. Additionally, we further searched for potential genomic regions in native chicken ecotypes, uncovering several candidate genes related to ecological adaptations affecting local breeds, such as IKBKB, S1PR1, TSHR, IL1RAPL1 and AMY2A, which are involved in disease resistance, heat tolerance, immune regulation and behavioral traits. This work provides important insights into the genomic characterization of ecotypes of native chicken in southern China. The identification of candidate genes associated with traits such as disease resistance, heat tolerance, immunomodulation, and behavioral traits is a significant outcome. These candidate genes may contribute to the understanding of the molecular basis of the adaptation of the southern native chicken to the local environment. It is recommended that these genes be integrated into chicken breeding programs to enhance sustainable agriculture and promote effective conservation and utilization strategies.

MiRNA-488-3p suppresses acute myocardial infarction-induced cardiomyocyte apoptosis via targeting ZNF791.

OBJECTIVE: The aim of this study was to elucidate the potential function of microRNA-488-3p (miRNA-488-3p) in the pathogenesis of acute myocardial infarction (AMI). MATERIALS AND METHODS: AMI mice constructed by ligation of the anterior descending coronary artery (LAD) were administrated with miRNA-488-3p mimics or negative control, respectively. Infarct size and risk region of AMI mice were determined by triphenyltetrazolium chloride (TTC) staining. The serum level of lactate dehydrogenase (LDH) release in mice was detected by enzyme-linked immunosorbent assay (ELISA). Subsequently, primary cardiomyocytes were isolated from AMI mice administrated with miRNA-488-3p mimics or negative control. LDH release in both hypoxia-preconditioning primary cardiomyocytes and MCM cells was detected. Dual-Luciferase reporter gene assay was used to verify the potential target of miRNA-488-3p. Furthermore, the regulatory effects of miRNA-488-3p and its target ZNF791 on AMI-induced cardiomyocyte apoptosis were evaluated. RESULTS: MiRNA-488-3p was lowly expressed in AMI mice. Meanwhile, miRNA-488-3p expression decreased in hypoxia-preconditioning primary cardiomyocytes or MCM cells in a time-dependent manner. AMI mice overexpressing miRNA-488-3p showed significantly smaller infarct size and risk region, as well as lower LHD release in serum. Overexpression of miRNA-488-3p markedly down-regulated the protein level of caspase3 in MCM cells. ZNF791 was predicted as the direct target of miRNA-488-3p, which was negatively regulated by miRNA-488-3p. Overexpression of ZNF791 reversed the protective role of miRNA-488-3p in AMI-induced cardiomyocyte apoptosis. CONCLUSIONS: MiRNA-488-3p is down-regulated in AMI mice, which alleviates AMI-induced cardiomyocyte apoptosis via down-regulating ZNF791.

Effects of Piper sarmentosum extract on the growth performance, antioxidant capability and immune response in weaned piglets.

The biological properties of Piper sarmentosum render it a potential substitute for antibiotics in livestock feed. This study evaluated the effects of P. sarmentosum extract (PSE) on the growth performance, antioxidant capability and immune response of weaned piglets. Eighty 21-d-old weaned piglets were selected and randomly allocated to one of four dietary treatments with five replicates of four pigs each. The dietary treatments consisted of a basal diet supplemented with 0 (T0), 50 (T50), 100 (T100) or 200 (T200) mg/kg PSE. The feeding trial lasted 4 weeks. The results revealed that the T50 group had the highest average daily gain (ADG) and average daily feed intake (ADFI) throughout the feeding trial (p < 0.05). Additionally, the T50 group had higher (p < 0.05) serum glutathione peroxidase activity (GSH-Px) and lower (p < 0.05) serum malondialdehyde (MDA) levels than the T0 group at 4 weeks post-weaning (p < 0.05). Serum levels of interleukin-1ß (IL-1ß) and tumour necrosis factor-α (TNF-α) decreased, while serum levels of interleukin-4 (IL-4), interleukin-10 (IL-10) and transforming growth factor-ß (TGF-ß) increased by PSE supplementation at 4 weeks post-weaning (p < 0.05). PSE supplementation upregulated the mRNA expression of IL-4, IL-10 and TGF-ß and downregulated the mRNA expression of TNF-α, IL-1ß and interleukin-6 (IL-6) in the ileal mucosal layer of piglets (p < 0.05). In summary, our study findings revealed that PSE supplementation improved the antioxidant capability, and reduced inflammation, which may be beneficial to weaned piglet health.

Investigation of TG gene variants and their effects on growth, carcass composition, and meat quality traits in Chinese steers.

Thyroid hormones play an important role in regulating metabolism and can affect metabolism-related traits such as fat deposition. The thyroglobulin (TG) gene produces the precursor of thyroid hormones and has been proposed as a candidate gene for a quantitative trait locus with an effect on fat deposition. In this study, we identified 4 novel single nucleotide polymorphisms (SNPs) in the 5' flanking region of the TG gene using a DNA sequencing method. The SNP marker association analysis indicated that the T1355C SNPs were significantly associated with meat percentage (P < 0.05). A significant association between the G1356A polymorphism and live weight and loin muscle area was also detected (P < 0.05). However, no significant association was found between 4 SNPs and the other growth, carcass composition, and meat quality traits including intramuscular fat. The results of this study suggest that TG gene-specific SNPs may be a useful marker for growth traits in marker-assisted selection programs in beef cattle.

Expression and variation of Myf5 and MyoD1 genes in different tissues of Wuzhishan pigs.

The myogenic regulatory factor (MRF) family includes Myf5, MyoD1, Myf4, and Mfy6 genes. This experiment assessed the variation of Myf5 and MyoD1 genes from birth to maturity (30, 210, and 360 days) in the back muscle tissue of Wuzhishan pigs (WZSP), and the expression of Myf5 and MyoD1 mRNA in the heart, liver, lung, spleen, kidney, muscle, stomach, and intestine tissues were also examined. The results indicate that the expression level of mRNA for Myf5 and MyoD1 genes in the back muscle tissue is directly proportional to age (P < 0.05). Furthermore, of the eight adult pig tissue types that were tested, the expression of Myf5 and MyoD1 was highest in the muscle tissue.

VEGF Trapon inhibits tumor growth in papillary thyroid carcinoma.

OBJECTIVE: Vascular endothelial growth factor (VEGF) is the most potent inducer of neovasculature, and its increased expression has been related to a worse clinical outcome in many disease. Angiogenesis from thyroid cancer cell plays the important roles in post-surgical persistent, recurrent, and metastatic papillary thyroid cancer (PTC). Vascular endothelial growth factor (VEGF) Trapon is a newly developed VEGF-blocking agent with stronger affinity and broader activity than the anti-VEGF antibody bevacizumab. In this study, we tested the activity of VEGF Trapon on a PTC model in vivo. MATERIALS AND METHODS: BC-PAP (derived from papillary carcinomas) transfected with a luciferase-expressing vector were injected into the back to mice. I.p. treatment with VEGF Trapon or control protein (25 mg/kg twice weekly) was started shortly after tumor injection to prevent tumor development (prevention model) or after established tumors were formed to inhibit tumor growth and metastasis formation (intervention model). RESULTS: In the prevention model, VEGF Trapon inhibited tumor growth by 73 ± 12% compared with control (p = 0.014) and significantly prolonged survival. In the intervention model, VEGF Trapon inhibited tumor growth by 68 ± 7% (p < 0.01). Microvascular density was reduced by 56% due to VEGF Trapon treatment (p < 0.01). CONCLUSIONS: VEGF Trapon is a potent inhibitor of BC-PAP tumor growth, angiogenesis and blocks the biological function of VEGF in vivo. These results support further clinical development of VEGF Trapon for PTC and other cancer types.

Soybean isoflavone reduces the residue of zearalenone in the muscle and liver of prepubertal gilts.

The aim of the present study was to evaluate the protective effects of isoflavone (ISO) against zearalenone (ZEA) residues in the muscle and liver tissues of prepubertal gilts. Seventy 75-day-old, prepubertal, female pigs (Duroc × Landrace × Yorkshire, 26.5 ± 0.60 kg) were allocated randomly to seven diet treatments for 21days as follows: one control group (fed the basal diet) and six groups fed the basal diet with the addition of either 0.5 or 2.0 mg/kg ZEA plus either 0, 300 or 600 mg/kg ISO. The results showed that the diet with 2.0 mg/kg ZEA added caused an increase of ZEA residue level in muscle tissue (P < 0.05), and that the addition of both 0.5 and 2.0 mg/kg ZEA increased the residue level of ZEA in the liver of prepubertal gilts (P < 0.05). Addition of 600 mg/kg ISO to 2.0 mg/kg ZEA-contaminated diet decreased the ZEA residue level in liver tissue (P < 0.05), and the addition of 300 or 600 mg/kg ISO to the 2.0 mg/kg ZEA-contaminated diet decreased the residue levels of ZEA in muscle tissue (P < 0.05). Western blot analysis demonstrated that feeding ZEA to prepubertal gilts increased their protein expression of 3α/3ß-hydroxysteroid dehydrogenase (HSD; P < 0.05), and that the addition of 300 or 600 mg/kg ISO to the 2.0 mg/kg ZEA-contaminated diet decreased the protein expression of 3α/3ß-HSD (P < 0.05), compared with the addition of 2.0 mg/kg ZEA alone. The results demonstrated that muscle and liver tissues retain residual ZEA when pigs are fed a diet contaminated with high concentrations of ZEA, and that the concentration of ZEA in muscle and liver tissues increased with increased amounts of ZEA in the feed. In diets contaminated with high levels of ZEA, the addition of ISO may accelerate the biotransformation and degradation of ZEA and its metabolites, and reduce the residues of ZEA in liver and muscle tissues of prepubertal gilts.

Detecting a deletion in the coding region of the bovine bone morphogenetic protein 15 gene (BMP15).

The aim of this study was to detect polymorphism in the bovine bone morphogenetic protein 15 (BMP15) gene. On the basis of PCR-SSCP and DNA sequencing, a 4-bp deletion was identified in the coding region of the gene. Sequence analysis revealed that the deletion altered the reading frame and introduced a stop codon at position 264. Eight breeds (Luxi, Qinchuan, Nanyang, Jinnan, Bohai Black, Menggolian, Holstein, and Simmental) were genotyped by PCR-SSCP. No cows homozygous for this mutation were observed in these breeds. Heterozygous cows were detected in Luxi, Qinchuan, Nanyang, Jinnan and Bohai Black cattle. Fecundity was not increased in heterozygous individuals.

Expression of human factor IX cDNA in mice by implants of genetically modified skin fibroblasts from a hemophilia B patient.

Double-copy retroviral vector containing human factor IX cDNA driven by human cytomegalovirus enhancer-promoter was constructed. The vector was introduced into the amphotropic packaging cell line PA317. The recombinant virus produced in PA317 was used to transduce skin fibroblasts from a hemophilia B patient. The infected cells produced high levels of biologically active human factor IX at a rate of 3420 ng/10(6) cells/24 h. These cells were embedded in a collagen matrix and implanted into the peritoneal cavity or subcutaneous space of mice. It was demonstrated that human factor IX was produced by the implants for at least 12 days in vivo, reaching a peak of 105 ng/ml plasma. Over 90% of the protein was functionally active. This technique has the potential to be developed into a new approach for gene therapy for hemophilia B.